Today marks nearing the completion of a full circle for one of science’s biggest controversies: the STAP cell fiasco. Today STAP cells are completely refuted with the publication of two new papers in Nature and we know much more–with some notable gaps still–about what went wrong.

In January of last year, an international team of collaborators from RIKEN in Japan and Harvard/Brigham & Women’s Hospital (including the lab of Charles Vacanti where the STAP idea reportedly originated) here in the US published two Nature papers making the extraordinary claim that ordinary cells could be reprogrammed into embryonic stem cell (ESC)-like cells.

And it could be done simply, cheaply, and quickly using various forms of cellular stress including low pH. I was highly skeptical when I read the papers, but tried to keep an open mind. This sounded cool, even if also too good to be true.

I published a review of the papers here on this blog on the day they were published and I included six key open questions that would be required to assess the real impact of these papers. Over the next few weeks I posted an increasingly skeptical series of posts questioning STAP.

Others in the larger community including anonymous scientific sleuth JuuichiJigen and some on PubPeer were skeptical as well. In fact, they started noticing issues with the data and text of the papers.

RIKEN and Nature began investigations. Ultimately the papers were retracted in relatively quick fashion. While a lot of harm was done even so and tragedy would strike later, the rapid refutation of STAP attenuated the overall damage.

I also started a novel, but admittedly somewhat basic attempt at crowdsourcingglobal efforts at STAP replication. Very quickly we came to a consensus that autofluorescence was likely a key stumbling point for the STAP papers as the authors probably misinterpreted it as real signal from a GFP pluripotency reporter.

Suspicions grew elsewhere that STAP cells might really be ESCs or some other pluripotent stem cells, possibly mixed with trophoblastic stem cells (TSC). Ultimately, STAP first author Haruko Obokata was found by RIKEN to have committed misconduct and she is no longer working at the institution. RIKEN underwent a big shakeup as a result of STAP as well. STAP co-author and highly respected biologist Yoshiki Sasai committed suicide, which was one of the most tragic and sobering events I’ve seen in science during my career. In Japan there had been a media frenzy on the STAP problems. In the US things on the STAP front were and continue to be quieter. As recently as about a year ago, Vacanti and co-author Koji Kojima publicly expressed complete confidence in STAP and put up a refined protocol on the web.

So what was the real deal with STAP?

Today Nature published two articles thoroughly refuting STAP cells and providing some further insights.

In one of the papers, STAP cells are derived from ES cells, the authors used whole genome sequencing (WGS) to examine archived STAP cell-related samples and other cells present in the laboratories where the STAP work was conducted. Using essentially a form of genomic fingerprinting, the team reports conclusive evidence that STAP cells were in actuality ESCs:

In summary, our investigations based on WGS of STAP-cell related materials reveal that all of these materials are derived from previously established ES cell lines and refute the evidence shown in the two Nature papersthat cellular stress can reprogram differentiated cells into pluripotent cells.

You can see Figure 1b from this study showing the WGS comparison that the genomic characteristics of various cell lines.

The matching patterns between two STAP-derived lines FLS3 and CTS1 and the supposedly unrelated FES1 ESC line are particularly striking. It now seems almost certain that a number of STAP cells are in reality FES1-related ESC lines and that the STAP cells were not created by cellular stress.

The other new paper from another team, Failure to replicate the STAP cell phenomenon, comes to similar conclusions and further clarity arises:

“In summary, our replication attempts and genetic analysis indicate that existing STAP protocols are neither robust nor reproducible. To substantiate future claims of reprogramming and alternative states of potency, we urge a rigorous application of several independent means for validating functional pluripotency and genomic profiling to confirm cell line provenance. Ultimately, the essential standard of robustness and reproducibility must be met for new claims to exert a positive and lasting influence on the research community.”

This second team led by George Daley at Brigham and Women’s spans the globe, but importantly they did some of the work actually in Vacanti’s lab, still finding no evidence that STAP is real. They wrote, “Working within the Vacanti laboratory where the concept of STAP cells originated, and assisted by a co-author of the STAP papers…”

Seven laboratories were involved in this second STAP replication effort: Daley, Deng, Hanna, Hochedlinger, Jaenisch, Pei and Wernig. This is an all-star team of stem cell research labs.

One bottom line from the paper is that this team collectively worked very hard to try to get STAP to work, but it didn’t:

Like the other team, these scientists analyzed the STAP cells including their genomes. They found inconsistencies between their new findings and the claims in the original STAP papers:

“In the original STAP reports, the authors stated that they mixed CD451 cells from male and female mice owing to the small number of CD451 cells retrieved from individual neonatal spleens. However, our analysis indicates that CD451 cells were female, whereas the derived cells (STAP cells, STAP stem cells and FI-SCs) were all male, a clear inconsistency.”

These authors also found indications of trophoblastic stem cells (TSC) being mixed into the STAP samples. TSC may explain the reported totipotency of some derivations of supposed STAP cells.

Nature itself explained why it published these new papers (in the Brief Communications Arising or BCA format):

“Why is Nature publishing these pieces? The main reason is to update the scientific record. The wording of the STAP retraction notices left open the possibility that the phenomenon was genuine. It said: “Multiple errors impair the credibility of the study as a whole and we are unable to say without doubt whether the STAP-SC phenomenon is real.” The two BCAs clearly establish that it is not.”

We are just about, but not quite at the end of the STAP story it seems. In my opinion there is still more to be learned about what went so wrong. How did the ESCs and in some cases TSCs end up in the cell culture mix? Accidental contamination? Intentional attempt to bolster the seductive hypothesis?

We may never know, but today there is a great deal more clarity overall at least.

The publication of these two new papers is a very positive step, but it is important to stress that absent post-publication review, rapid and open team science, and social media efforts, the STAP cell myth may have continued to have been believed by many in the research world until this day when these debunking papers were published. That delay would likely have caused immeasurable damage. Thus, there were important roles both for traditional scientific correction via journals and new, transformative types of rapid post-publication review.

6 Comments

Nature still hasn’t explained the details of the editorial process that led to publication of the STAP papers. Although in hindsight publication was clearly inappropriate, Nature should release information to show whether or not acceptance of these papers for publication was reasonable based on the information available to the editor at the time the decision was made.

Why would they not test STAP cell phenomenon by using adenosine triphosphate listed in a patent(WO/2013/163296)?
Dr. Niwa saw the expression of pluripotent marker and unknown behavior and cell’s death using ATP they said to the media on 19 Dec,2014. (http://www.riken.jp/pr/topics/2014/20141219_1/)

Dr.Obokata made STAP-cells using ATP, Physical stimulation, HCl, but Dr.Katsura ( National Institute of Genetics, Japan ) said to Japanese media that when Dr.Sasai revised, He wrote HCl only in the article and the letter on 26 Dec,2014.

I do not know why RIKEN said FLS ESCs (doi:10.1038/nature15366) are B6129F1♂, Dr.Wakayama said FLS ESCs are 129B6F1♂ at the same time on 16 June,2014.

Riken received FLS ESCs (doi:10.1038/nature15366) in 2014 from Dr. Hiroshi Ota ( Kyoto Univ, in RIKEN CDB Dr.Wakayama’s labo until 2010. http://www.nikkei-science.com/201503_034.html ) and analyzed them and the investigative committee held a press conference without the foreign media on 26 Dec,2014 ( http://www.riken.jp/pr/topics/2014/20141226_1/ ), But the citizens cannot discover objective evidence from archives that FLS ESCs were certainly in Kyoto Univ.

Riken received ESCs except FLS ESCs (doi:10.1038/nature15366) from Wakayama-labo that never closed in Yamanashi University in 2014 and analyzed. Unfortunately ESCs from the labo are not preserve Evidence.

Japanese academia believed the news from Dr.Endo A Takaho’s STAP cells are ESCs ( http://www.nikkei-science.com/wp-content/uploads/2014/06/20140611STAP.pdf ) on 20 June,2014 and RIKEN reform committee criticized Dr.Sasai and Dr.Obokata who really want replication intensely, so they might hope that its were ESCs. Dr.Endo A Takaho’s Article (http://onlinelibrary.wiley.com/doi/10.1111/gtc.12178/full ) published on 21 SEP,2014, Dr.Obokata mixed cells of fetus mice (about 3 mice) and soaked in acid or ATP to made STAP cells but Dr.Endo said ratio of chromosome8 mRNA data by SMARTer®, show trisomy8. Dr.Endo said with his blog STAP cells are ESCs by CNV (ChIP-seq) on 11 March,2014 ( http://srad.jp/~kaho/journal ) and many young Japanese scientists filled with passionate indignation but it was rejected by Nature in April,2014.

Dr.Wakayama made the chimera mice, STAP stem cells and FI stem cells so Dr.Obokata ( Engineering,2011 ) do not know what they did. She got mice from animal handlers of Wakayama-labo. She got a wrong very many photographs. Some people are doubting visual agnosia.

“Riken received ES cells except FES and ntES (doi:10.1038/nature15366) from Wakayama-labo that never closed in Yamanashi University in 2014 and analyzed. Unfortunately ES cells from the labo are not preserved Evidence.”

Why did Nature publish this? As mentioned in the post, they rejected a failed replication under “unclear” reasoning.
The overall scientific conclusions in the paper are well-known at this point. I thought Nature encouraged breakthrough science. But, if submitted from the right labs, something already published and widely accepted qualifies?
I really actually wish STAP drama to end out of fatigue, but I can’t help but think this publication signifies another flaw with Nature leadership.

Contrary to what Jacob Hanna said about social media being irrelevant, I disagree. STAP maybe exceptional, as there are many reprogramming labs who can attempt replication, but without the communication and attention of social media, it would remain dubious.
As a reader, the social media did matter to my perception and information about the papers a great deal. In contrast, the new paper Hanna happens to be an author in, did nothing to inform me or change my understanding.

Just as a disclaimer, I think there was a downside to unmoderated negative comments. Even though skeptics proved right, IMO the conclusions were reached early to to prevailing cynicism. Speaking as a long time admirer of Dr. Yoshiki Sasai, I hope our scientific interest do not lead to undue non-scientific, personal problems in the future.